Group Beta Streptococcus and Neisseria meningitidis are leading causes of neonatal sepsis and meningitis. The increasing use of carbohydrate-based conjugate vaccines is founded on the observation that antibodies against the type-specific bacterial capsular polysaccharides (CPS) are often protective, and-is driven by the increasing prevalence of antibiotic resistant strains. However, the relationships between the carbohydrate sequence in the CPS and antigenicity are poorly understood. Similarly, the immune response to the CPS is structure-sensitive; some are poor immunogens and others good. The goal of this proposal is to provide an understanding of the structural features of antigenic oligosaccharides that are responsible for mediating the affinity and specificity of their interactions with antibodies. Ultimately, this information would form a basis for the rational development of more effective antibacterial vaccines. We have selected three systems (Aims 1-3) for study that display complementary levels of complexity. In Aims 1 and 2, we will use computational and experimental methods to determine the conformational properties of the bacterial CPSs from iV. meningitides and Group B Streptococcus, both free and bound to monoclonal antibody fragments. This information will provide a structural basis for interpreting the antigenicities and antibody specificities for these systems, as well as assist in the determination of the conformation of the immunodominant regions. To aid in the development and validation of the computational methods, in Aim 3, we will examine the properties of the related anionic sugars in glycosaminoglycans (GAGs), for which considerable experimental data exist. Computational methods, such as molecular dynamics (MD) simulations, are useful aids in the conformationat analysis of oligosaccharides and oligosaccharide-protein complexes; yet at present they have been developed only for neutral carbohydrates. The CPSs from N. meningitides and Group B Streptococcus, and from many other pathogenic bacteria, contain anionic carbohydrate residues. Accurate modeling of these molecules will require the extension and validation of our existing carbohydrate force field parameters (GLYCAM). To assist in this development, we will examine a number of anionic GAGs, such as hyaluronan, chondroitin and heparin sulfate as well as heparin, free and complexed to antithrombin III, whose conformational properties have been well characterized experimentally. Validation of the MD simulations will be based on comparisons with NMR and X-ray data and binding affinity measurements.